Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

N.A. Rosenberg, T. Burke, K. Elo, M.W. Feldman, P.J. Friedlin, M.A.M. Groenen, J. Hillel, A. Maki-Tanila, M. Tixier-Boichard, A. Vignal, K. Wimmers

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270 Citations (Scopus)

Abstract

We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently ∼98ÐWhen markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95␌lustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90ÐWe suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.
Original languageEnglish
Pages (from-to)699-713
JournalGenetics
Volume159
Publication statusPublished - 2001

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    Rosenberg, N. A., Burke, T., Elo, K., Feldman, M. W., Friedlin, P. J., Groenen, M. A. M., ... Wimmers, K. (2001). Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics, 159, 699-713.